Global concerns regarding microplastics emerging in the environment have been raised recently. Using samples collected during the OceanXplorer mission in Aqaba, we explored the depth-based and regional variations of microplastics across pelagic and benthic zones. Microplastics (63.0–950.0 μm) from the surface seawater, middle seawater, bottom seawater, and deep-sea sediment were quantified and identified using a dissecting microscope and Fourier Transform Infrared microscope (μ-FTIR). The results revealed that the average abundance of microplastics was 6.7 ± 6.05 particles L⁻¹ in the pelagic zone and 2900 ± 1650 particles kg⁻¹ in the benthic zone. A size gradation of microplastics was observed across depths from 5 to 840 m, accompanied by a shift in particle types: fragments were the most common in the benthic zone, whereas fibers dominated the pelagic zone. μ-FTIR analysis identified the presence of the following polymers: polyethylene (PE), polyvinyl chloride (PVC), polyamide 6 (PA 6), and polypropylene (PP). These findings establish baseline data for future monitoring and management efforts addressing microplastic pollution in the Gulf of Aqaba.